sgRNA Scorer 1.0

Welcome to sgRNA Scorer 1.0. Given an input sequence or list of sequences, our interactive web tool will identify putative CRISPR/Cas9 sites for either Cas9 from S. pyogenes (PAM: NGG) or S. thermophilus (PAM: NNAGAAW) and assign a predicted activity based on our support vector machine model. The models were generated using data from our experiments in 293T cells which can be found in Supplementary Data 10 for Cas9 S. pyogenes and Supplementary Data 12 for Cas9 S. thermophilus. In addition, an option exists to select sites with minimal off-target activity based on the CasFinder algorithm as well, enabling target sites to be selected with high predicted specificity and activity.

We have also made available a pre-computed list of sites derived using CasFinder and scored with sgRNA Scorer for the entire human and mouse exomes for both Cas9 orthologs. This can be found here.

Please use a working e-mail address as a link to a file with results from sgRNA scorer will be emailed to you as soon as it's done. The file will be retained for 24 hours.


E-mail address:

Cas9 Ortholog:

Select input (paste sequence or upload file, FASTA format, limit to 10 kb of sequence total). Example of an input file can be found here.
If pasting sequences, ensure the first line starts with '>', with a sequence name, and then the sequence itself (i.e.>SequenceName[return]sequence[return]). Look at the example file for exact format when pasting in. Please use a minimum sequence size of 30 bp.

Paste sequence

Upload file
Run CasFinder off-target analysis?

Citing our tool:
Chari R, Mali P, Moosburner M, Church GM (2015). Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nature Methods 12(9):823-6. PMID: 26167643.

If you use the CasFinder functionality as well, please cite:
Aach J, Mali P, Church GM (2014). CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv.

The standalone version of this software can be found here.

Any suggestions or comments can be e-mailed to sgRNAScorer 'at' hms 'dot' harvard 'dot' edu

Updated February 25th, 2016